You can get the keys into a separate table and then sort that table using the criteria you need:
local t = {
a = {1,2},
b = {2,3},
c = {4,1},
d = {9,9},
}
local keys = {}
for k in pairs(t) do table.insert(keys, k) end
table.sort(keys, function(a, b) return t[a][2] > t[b][2] end)
for _, k in ipairs(keys) do print(k, t[k][1], t[k][2]) end
will print:
d 9 9
b 2 3
a 1 2
c 4 1